{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/4c796e96f552404e6e25601213be659b/hermann", "tags" : [ "forschungsdaten","assessment","documentation","software" ], "intraHash" : "4c796e96f552404e6e25601213be659b", "label" : "Rate your Project", "user" : "hermann", "description" : "A self assessment tool for improving software practices\r\n\r\nSoftware engineering is a systematic approach to the design, development, and maintenance of a software system. Teams seldom have the time to stop development and focus solely on improving productivity or sustainability. However, teams can incorporate improvements on the way to developing new science capabilities.\r\n\r\nThe tools on this site will help you:\r\n\r\nAssess your current practices\r\nCreate progress tracking cards\r\nIntegrate tracking cards with your workflow\r\nThe self-assessment introduces software engineering practices that increase in maturity. Check the practices that your project already uses to rate your project.\r\n\r\nTake the survey by clicking the button below or sign in to customize your survey and save the results directly to your project repository!", "date" : "2024-02-08 13:25:48", "changeDate" : "2024-02-08 13:25:48", "count" : 1, "url" : "https://rateyourproject.org" } , { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/1374c21024e7fb19b8d7c94ae8d5c2a8/hermann", "tags" : [ "documentation","agil","software" ], "intraHash" : "1374c21024e7fb19b8d7c94ae8d5c2a8", "label" : "Technical Documentation in Software Development: Types, Best Practices, and Tools", "user" : "hermann", "description" : "", "date" : "2021-03-16 06:31:58", "changeDate" : "2021-03-16 05:31:58", "count" : 1, "url" : "https://www.altexsoft.com/blog/business/technical-documentation-in-software-development-types-best-practices-and-tools/" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/27f281edbd2f7ba5d5ae07a239810e68c/hermann", "tags" : [ "documentation","software","diss" ], "intraHash" : "7f281edbd2f7ba5d5ae07a239810e68c", "interHash" : "5db5f91bf9bab54fe6a2e4aa2185e9ee", "label" : "Software engineering at Google: lessons learned from programming over time", "user" : "hermann", "description" : "", "date" : "2022-07-27 10:03:53", "changeDate" : "2022-07-27 08:03:53", "count" : 1, "pub-type": "book", "publisher":"O'Reilly","address":"Beijing", "year": "2020", "url": "", "author": [ "Titus Winters","Tom Manshreck","Wright Hyrum" ], "authors": [ {"first" : "Titus", "last" : "Winters"}, {"first" : "Tom", "last" : "Manshreck"}, {"first" : "Wright", "last" : "Hyrum"} ], "note": "1 Online Ressource (xxv, 571 pages)", "isbn" : "978-1-4920-8276-7", "language" : "Englisch", "bibtexKey": "Winters2020Softwareengineering" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/23210e1ffc832fafc1dca203bc6d8869d/hermann", "tags" : [ "documentation","workflow","diss" ], "intraHash" : "3210e1ffc832fafc1dca203bc6d8869d", "interHash" : "a3e47a18268aab24f08bfe75e91190cb", "label" : "Docs for Developers", "user" : "hermann", "description" : "", "date" : "2022-05-02 11:10:23", "changeDate" : "2022-05-02 09:10:23", "count" : 1, "pub-type": "book", "publisher":"Apress", "year": "2021", "url": "https://doi.org/10.1007%2F978-1-4842-7217-6", "author": [ "Jared Bhatti","Zachary Sarah Corleissen","Jen Lambourne","David Nunez","Heidi Waterhouse" ], "authors": [ {"first" : "Jared", "last" : "Bhatti"}, {"first" : "Zachary Sarah", "last" : "Corleissen"}, {"first" : "Jen", "last" : "Lambourne"}, {"first" : "David", "last" : "Nunez"}, {"first" : "Heidi", "last" : "Waterhouse"} ], "doi" : "10.1007/978-1-4842-7217-6", "bibtexKey": "bhatti2021developers" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22f2ee5301ce94996363f6f8863bfdf6e/hermann", "tags" : [ "documentation","Gedächtnis","lernen" ], "intraHash" : "2f2ee5301ce94996363f6f8863bfdf6e", "interHash" : "550af74d59660f47da7b019637fecfa6", "label" : "On the Symbiosis of Remembering, Forgetting and Learning", "user" : "hermann", "description" : "", "date" : "2022-02-07 16:12:04", "changeDate" : "2022-02-07 15:12:04", "count" : 1, "pub-type": "inbook", "booktitle": "Successful remembering and successful forgetting : a Festschrift in honor of Robert A. Bjork","publisher":"Psychology Press","address":"New York, NY [u.a.]", "year": "2011", "url": "http://swbplus.bsz-bw.de/bsz33072066Xinh.htm", "author": [ "R.A. Bjork" ], "authors": [ {"first" : "R.A.", "last" : "Bjork"} ], "editor": [ "Aaron S. Benjamin","Robert A. Bjork" ], "editors": [ {"first" : "Aaron S.", "last" : "Benjamin"}, {"first" : "Robert A.", "last" : "Bjork"} ], "note": "Literaturangaben; Mit Reg.; \"In January 2009, the University of California, Los Angeles hosted a conference in which only a small portion of the many friends, mentors, colleagues, and students of Robert Bjork came together to discuss current research on human memory and to celebrate together the many traditions and friendships that mark Bob's career.\" (Preface, p. XI)Erscheint: 01. November 2010; On the symbiosis of remembering, forgetting, and learning; Intricacies of spaced retrieval : a resolution; Distributed learning and the size of memory : a 50-year spacing odyssey; The causes and consequences of reminding; Retrieval-induced forgetting and the resolution of competition; On the relationship between interference and inhibition in cognition; Sleep, retrieval inhibition, and the resolving power of human memory; Blocking out blocks : adaptive forgetting of fixation in memory, problem solving, and creative ideation; A contextual framework for understanding when difficulties are desirable; Testing, generation, and spacing applied to education : past, present, and future; Learning from and for tests; Can desirable difficulties overcome deceptive clarity in scientific visualizations?; Desirable difficulties and studying in the region of proximal learning; Data entry : a window to principles of training; An output-bound perspective on false memories : the case of the Deese Roediger McDermott (DRM) paradigm; How should we define and differentiate metacognitions?; Learning from the consequences of retrieval : another test effect; Failing to predict future changes in memory : a stability bias yields long-term overconfidence; Relying on other people's metamemory; Multidimensional models for item recognition and source identification; Pursuing a general model of recall and recognition; Memory for pictures : sometimes a picture is not worth a single word; Administration of dehydroepiandrosterone (DHEA) increases serum levels of androgens and estrogens but does not enhance recognition memory in postmenopausal women; On the fruitful relationship between functional neuroimaging and cognitive theories of human learning and memory; Age-related changes in the episodic simulation of past and future events", "isbn" : "9781848728912; 1848728913", "bibtexKey": "Bjork2011successful" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24c6417d0d82be245a908bfd13c0b1e78/hermann", "tags" : [ "forschungsdaten","documentation","software" ], "intraHash" : "4c6417d0d82be245a908bfd13c0b1e78", "interHash" : "fef517974b15bda533222611846ebee7", "label" : "Four simple recommendations to encourage best practices in research software", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:40:06", "changeDate" : "2021-06-05 15:11:18", "count" : 1, "pub-type": "article", "journal": "F1000Research","publisher":"F1000 Research Ltd", "year": "2017", "url": "https://doi.org/10.12688%2Ff1000research.11407.1", "author": [ "Rafael C. Jiménez","Mateusz Kuzak","Monther Alhamdoosh","Michelle Barker","Bérénice Batut","Mikael Borg","Salvador Capella-Gutierrez","Neil Chue Hong","Martin Cook","Manuel Corpas","Madison Flannery","Leyla Garcia","Josep Ll. Gelp\\'ı","Simon Gladman","Carole Goble","Montserrat González Ferreiro","Alejandra Gonzalez-Beltran","Philippa C. Griffin","Björn Grüning","Jonas Hagberg","Petr Holub","Rob Hooft","Jon Ison","Daniel S. Katz","Brane Leskosek","Federico López Gómez","Luis J. Oliveira","David Mellor","Rowland Mosbergen","Nicola Mulder","Yasset Perez-Riverol","Robert Pergl","Horst Pichler","Bernard Pope","Ferran Sanz","Maria V. Schneider","Victoria Stodden","Radosław Suchecki","Radka Svobodová Vareková","Harry-Anton Talvik","Ilian Todorov","Andrew Treloar","Sonika Tyagi","Maarten van Gompel","Daniel Vaughan","Allegra Via","Xiaochuan Wang","Nathan S. Watson-Haigh","Steve Crouch" ], "authors": [ {"first" : "Rafael C.", "last" : "Jiménez"}, {"first" : "Mateusz", "last" : "Kuzak"}, {"first" : "Monther", "last" : "Alhamdoosh"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Bérénice", "last" : "Batut"}, {"first" : "Mikael", "last" : "Borg"}, {"first" : "Salvador", "last" : "Capella-Gutierrez"}, {"first" : "Neil Chue", "last" : "Hong"}, {"first" : "Martin", "last" : "Cook"}, {"first" : "Manuel", "last" : "Corpas"}, {"first" : "Madison", "last" : "Flannery"}, {"first" : "Leyla", "last" : "Garcia"}, {"first" : "Josep Ll.", "last" : "Gelp\\'ı"}, {"first" : "Simon", "last" : "Gladman"}, {"first" : "Carole", "last" : "Goble"}, {"first" : "Montserrat González", "last" : "Ferreiro"}, {"first" : "Alejandra", "last" : "Gonzalez-Beltran"}, {"first" : "Philippa C.", "last" : "Griffin"}, {"first" : "Björn", "last" : "Grüning"}, {"first" : "Jonas", "last" : "Hagberg"}, {"first" : "Petr", "last" : "Holub"}, {"first" : "Rob", "last" : "Hooft"}, {"first" : "Jon", "last" : "Ison"}, {"first" : "Daniel S.", "last" : "Katz"}, {"first" : "Brane", "last" : "Leskosek"}, {"first" : "Federico López", "last" : "Gómez"}, {"first" : "Luis J.", "last" : "Oliveira"}, {"first" : "David", "last" : "Mellor"}, {"first" : "Rowland", "last" : "Mosbergen"}, {"first" : "Nicola", "last" : "Mulder"}, {"first" : "Yasset", "last" : "Perez-Riverol"}, {"first" : "Robert", "last" : "Pergl"}, {"first" : "Horst", "last" : "Pichler"}, {"first" : "Bernard", "last" : "Pope"}, {"first" : "Ferran", "last" : "Sanz"}, {"first" : "Maria V.", "last" : "Schneider"}, {"first" : "Victoria", "last" : "Stodden"}, {"first" : "Radosław", "last" : "Suchecki"}, {"first" : "Radka Svobodová", "last" : "Vareková"}, {"first" : "Harry-Anton", "last" : "Talvik"}, {"first" : "Ilian", "last" : "Todorov"}, {"first" : "Andrew", "last" : "Treloar"}, {"first" : "Sonika", "last" : "Tyagi"}, {"first" : "Maarten", "last" : "van Gompel"}, {"first" : "Daniel", "last" : "Vaughan"}, {"first" : "Allegra", "last" : "Via"}, {"first" : "Xiaochuan", "last" : "Wang"}, {"first" : "Nathan S.", "last" : "Watson-Haigh"}, {"first" : "Steve", "last" : "Crouch"} ], "volume": "6","pages": "876", "doi" : "10.12688/f1000research.11407.1", "bibtexKey": "jimenez2017simple" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c339bc95af1451e1bfa414d3e063f714/hermann", "tags" : [ "forschungsdaten","documentation","software","recommendation","diss" ], "intraHash" : "c339bc95af1451e1bfa414d3e063f714", "interHash" : "f3537561d112ec6aa23e044f853131f4", "label" : "Ten recommendations for software engineering in research", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:24:06", "changeDate" : "2021-05-27 12:41:49", "count" : 1, "pub-type": "article", "journal": "GIGASCIENCE","publisher":"BIOMED CENTRAL LTD","address":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND", "year": "2014", "url": "", "author": [ "Janna Hastings","Kenneth Haug","Christoph Steinbeck" ], "authors": [ {"first" : "Janna", "last" : "Hastings"}, {"first" : "Kenneth", "last" : "Haug"}, {"first" : "Christoph", "last" : "Steinbeck"} ], "volume": "3","abstract": "Research in the context of data-driven science requires a backbone of\r\n well-written software, but scientific researchers are typically not\r\n trained at length in software engineering, the principles for creating\r\n better software products. To address this gap, in particular for young\r\n researchers new to programming, we give ten recommendations to ensure\r\n the usability, sustainability and practicality of research software.", "author-email" : "hastings@ebi.ac.uk", "language" : "English", "researcherid-numbers" : "Haug, Ove Kenneth/O-3809-2019\r\n Haug, Kenneth/AAD-4241-2019\r\n Haug, Ove Kenneth/D-8694-2017", "oa" : "DOAJ Gold, Green Published", "affiliation" : "Hastings, J (Corresponding Author), European Bioinformat Inst, European Mol Biol Lab, Cheminformat & Metab, Wellcome Trust Genome Campus, Hinxton CB10 1SD, England.\r\n Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph, European Bioinformat Inst, European Mol Biol Lab, Cheminformat & Metab, Hinxton CB10 1SD, England.", "usage-count-last-180-days" : "0", "web-of-science-categories" : "Biology; Multidisciplinary Sciences", "article-number" : "31", "number-of-cited-references" : "12", "research-areas" : "Life Sciences & Biomedicine - Other Topics; Science & Technology -\r\n Other Topics", "eissn" : "2047-217X", "times-cited" : "4", "orcid-numbers" : "Haug, Ove Kenneth/0000-0003-3168-4145\r\n Hastings, Janna/0000-0002-3469-4923\r\n Steinbeck, Christoph/0000-0001-6966-0814", "usage-count-since-2013" : "8", "doc-delivery-number" : "CX4HC", "da" : "2021-05-27", "journal-iso" : "GigaScience", "unique-id" : "ISI:000365658900002", "doi" : "10.1186/2047-217X-3-31", "bibtexKey": "hastings2014recommendations" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b3444488cffac8a5783daba56155426a/hermann", "tags" : [ "forschungsdaten","documentation","software","recommendation","diss" ], "intraHash" : "b3444488cffac8a5783daba56155426a", "interHash" : "5a71f8c7107551d18a1a9903e96ddc4d", "label" : "Ten simple rules for making research software more robust", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:15:39", "changeDate" : "2021-05-27 12:41:59", "count" : 3, "pub-type": "article", "journal": "PLOS Computational Biology","publisher":"Public Library of Science", "year": "2017", "url": "https://doi.org/10.1371/journal.pcbi.1005412", "author": [ "Morgan Taschuk","Greg Wilson" ], "authors": [ {"first" : "Morgan", "last" : "Taschuk"}, {"first" : "Greg", "last" : "Wilson"} ], "volume": "13","number": "4","pages": "1-10","abstract": "Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer\u2019s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.", "doi" : "10.1371/journal.pcbi.1005412", "bibtexKey": "taschuk2017simple" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/26d2f38b8cd5017445fc76985fb30e93d/hermann", "tags" : [ "forschungsdaten","documentation","software" ], "intraHash" : "6d2f38b8cd5017445fc76985fb30e93d", "interHash" : "1ddaff170b5ac569bfdcbb3c06dad363", "label" : "Top considerations for creating bioinformatics software documentation", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:05:13", "changeDate" : "2021-05-27 12:05:13", "count" : 2, "pub-type": "article", "journal": "BRIEFINGS IN BIOINFORMATICS","publisher":"OXFORD UNIV PRESS","address":"GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND", "year": "2018", "url": "", "author": [ "Mehran Karimzadeh","Michael M. Hoffman" ], "authors": [ {"first" : "Mehran", "last" : "Karimzadeh"}, {"first" : "Michael M.", "last" : "Hoffman"} ], "volume": "19","number": "4","pages": "693-699","abstract": "Investing in documenting your bioinformatics software well can increase\r\n its impact and save your time. To maximize the effectiveness of your\r\n documentation, we suggest following a few guidelines we propose here. We\r\n recommend providing multiple avenues for users to use your research\r\n software, including a navigable HTML interface with a quick start,\r\n useful help messages with detailed explanation and thorough examples for\r\n each feature of your software. By following these guidelines, you can\r\n assure that your hard work maximally benefits yourself and others.", "author-email" : "michael.hoffman@utoronto.ca", "language" : "English", "researcherid-numbers" : "Hoffman, Michael M./I-1924-2012", "oa" : "Green Published, Green Accepted, Other Gold", "affiliation" : "Hoffman, MM (Corresponding Author), Princess Margaret Canc Ctr, Toronto Med Discovery Tower 11-311,101 Coll St, Toronto, ON M5G 1L7, Canada.\r\n Hoffman, Michael M., Princess Margaret Canc Ctr, Toronto Med Discovery Tower 11-311,101 Coll St, Toronto, ON M5G 1L7, Canada.\r\n Karimzadeh, Mehran; Hoffman, Michael M., Univ Toronto, Dept Med Biophys, Toronto, ON, Canada.\r\n Hoffman, Michael M., Univ Toronto, Dept Comp Sci, Toronto, ON, Canada.", "usage-count-last-180-days" : "0", "web-of-science-categories" : "Biochemical Research Methods; Mathematical & Computational Biology", "number-of-cited-references" : "40", "research-areas" : "Biochemistry & Molecular Biology; Mathematical & Computational Biology", "eissn" : "1477-4054", "funding-text" : "The Canadian Cancer Society (703827 to M.M.H.), the Ontario Institute\r\n for Cancer Research (OICR), the Natural Sciences and Engineering\r\n Research Council of Canada (RGPIN-2015-03948 to M.M.H.), the Ontario\r\n Ministry of Research, Innovation and Science (ER-15-11-223 to M.M.H.),\r\n the University of Toronto McLaughlin Centre (MC-2015-16 to M.M.H.) and\r\n the Princess Margaret Cancer Foundation.", "funding-acknowledgement" : "Canadian Cancer SocietyCanadian Cancer Society (CCS) [703827]; Ontario\r\n Institute for Cancer Research (OICR); Natural Sciences and Engineering\r\n Research Council of CanadaNatural Sciences and Engineering Research\r\n Council of Canada (NSERC)CGIAR [RGPIN-2015-03948]; Ontario Ministry of\r\n Research, Innovation and Science [ER-15-11-223]; University of Toronto\r\n McLaughlin Centre [MC-2015-16]; Princess Margaret Cancer\r\n FoundationUniversity of Toronto", "times-cited" : "7", "issn" : "1467-5463", "orcid-numbers" : "Hoffman, Michael M./0000-0002-4517-1562\r\n Karimzadeh, Mehran/0000-0002-7324-6074", "usage-count-since-2013" : "2", "doc-delivery-number" : "GP9NI", "da" : "2021-05-27", "journal-iso" : "Brief. Bioinform.", "keywords-plus" : "DIFFERENTIAL EXPRESSION ANALYSIS; READ ALIGNMENT; SEQUENCE;\r\n BIOCONDUCTOR; GENERATION; BENEFITS; QUALITY; SUITE; TOOL; DNA", "unique-id" : "ISI:000441243300014", "doi" : "10.1093/bib/bbw134", "bibtexKey": "karimzadeh2018considerations" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/235c906e6e0ed8af37317e03e45d8d101/hermann", "tags" : [ "forschungsdaten","documentation","software","diss","quality" ], "intraHash" : "35c906e6e0ed8af37317e03e45d8d101", "interHash" : "e7cf2e3e9da28d4a81f902d6e27553c5", "label" : "Software Engineering at Google", "user" : "hermann", "description" : "", "date" : "2021-04-13 07:03:21", "changeDate" : "2021-04-13 05:03:21", "count" : 2, "pub-type": "article", "journal": "CoRR", "year": "2017", "url": "http://arxiv.org/abs/1702.01715", "author": [ "Fergus Henderson" ], "authors": [ {"first" : "Fergus", "last" : "Henderson"} ], "volume": "abs/1702.01715", "eprint" : "1702.01715", "bibsource" : "dblp computer science bibliography, https://dblp.org", "archiveprefix" : "arXiv", "bibtexKey": "henderson2017software" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b1b8a9aa87b52be1c120d24b6fe67fb9/hermann", "tags" : [ "forschungsdaten","documentation","software","diss" ], "intraHash" : "b1b8a9aa87b52be1c120d24b6fe67fb9", "interHash" : "ebd33778680af00f3b38528ba05f9700", "label" : "Software Engineering for Computational Science: Past, Present, Future", "user" : "hermann", "description" : "", "date" : "2021-04-13 06:51:12", "changeDate" : "2021-04-13 04:51:12", "count" : 1, "pub-type": "article", "journal": "Computing in Science Engineering", "year": "2018", "url": "https://ieeexplore.ieee.org/document/8317991/", "author": [ "Arne Johanson","Wilhelm Hasselbring" ], "authors": [ {"first" : "Arne", "last" : "Johanson"}, {"first" : "Wilhelm", "last" : "Hasselbring"} ], "volume": "20","number": "2","pages": "90-109","abstract": "Despite the increasing importance of in silico experiments to the scientific discovery process, state-of-the-art software engineering practices are rarely adopted in computational science. To understand the underlying causes for this situation and to identify ways to improve it, the authors conducted a literature survey on software engineering practices in computational science. They identified 13 recurring key characteristics of scientific software development that are the result of the nature of scientific challenges, the limitations of computers, and the cultural environment of scientific software development. Their findings allow them to point out shortcomings of existing approaches for bridging the gap between software engineering and computational science and to provide an outlook on promising research directions that could contribute to improving the current situation.", "issn" : "1558-366X", "doi" : "10.1109/MCSE.2018.021651343", "bibtexKey": "johanson2018software" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2af0885a34e9bf1a950b4ccdb3b89bf2c/hermann", "tags" : [ "forschungsdaten","documentation","software","diss" ], "intraHash" : "af0885a34e9bf1a950b4ccdb3b89bf2c", "interHash" : "3c8beb3be2b3585468268a7eb6ceef7f", "label" : "The Roles of Code in Computational Science", "user" : "hermann", "description" : "", "date" : "2021-04-13 06:49:30", "changeDate" : "2021-04-13 04:49:30", "count" : 2, "pub-type": "article", "journal": "Computing in Science Engineering", "year": "2017", "url": "https://ieeexplore.ieee.org/document/7802531/", "author": [ "Konrad Hinsen" ], "authors": [ {"first" : "Konrad", "last" : "Hinsen"} ], "volume": "19","number": "1","pages": "78-82","abstract": "Many of us write code regularly as part of our scientific activity, perhaps even as a full-time job. But even though we write--and use--more and more code, we rarely think about the roles that this code will have in our research, in our publications, and ultimately in the scientific record. In this article, the author outlines some frequent roles of code in computational science. These roles aren't exclusive; in fact, it's common for a piece of code to have several roles, at the same time or as an evolution over time. Thinking about these roles, ideally before starting to write the code, is a good habit to develop.", "issn" : "1558-366X", "doi" : "10.1109/MCSE.2017.18", "bibtexKey": "hinsen2017roles" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/289ca6df04bbf38567e94cb2e05fed0c4/hermann", "tags" : [ "forschungsdaten","documentation","software","diss","quality" ], "intraHash" : "89ca6df04bbf38567e94cb2e05fed0c4", "interHash" : "722f4da160c40f832cecac27e437ab4f", "label" : "Software reliability modeling based on ISO/IEC SQuaRE", "user" : "hermann", "description" : "", "date" : "2021-03-11 06:28:02", "changeDate" : "2021-03-11 05:28:02", "count" : 2, "pub-type": "article", "journal": "Information and Software Technology","publisher":"Elsevier BV", "year": "2016", "url": "https://doi.org/10.1016%2Fj.infsof.2015.09.006", "author": [ "Felipe Febrero","Coral Calero","M. Ángeles Moraga" ], "authors": [ {"first" : "Felipe", "last" : "Febrero"}, {"first" : "Coral", "last" : "Calero"}, {"first" : "M. Ángeles", "last" : "Moraga"} ], "volume": "70","pages": "18--29", "doi" : "10.1016/j.infsof.2015.09.006", "bibtexKey": "Febrero_2016" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f6dbb3004ea1bb6414aadcce70225900/hermann", "tags" : [ "forschungsdaten","documentation","software","reusability","diss" ], "intraHash" : "f6dbb3004ea1bb6414aadcce70225900", "interHash" : "3dace87e232cc43887d37e9e3814f0a7", "label" : "Open science in practice: Learning integrated modeling of coupled\r\n surface-subsurface flow processes from scratch", "user" : "hermann", "description" : "", "date" : "2021-03-01 06:50:48", "changeDate" : "2021-03-01 05:50:48", "count" : 1, "pub-type": "article", "journal": "EARTH AND SPACE SCIENCE","publisher":"AMER GEOPHYSICAL UNION","address":"2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA", "year": "2016", "url": "", "author": [ "Xuan Yu","Christopher J. Duffy","Alain N. Rousseau","Gopal Bhatt","Alvaro Pardo Alvarez","Dominique Charron" ], "authors": [ {"first" : "Xuan", "last" : "Yu"}, {"first" : "Christopher J.", "last" : "Duffy"}, {"first" : "Alain N.", "last" : "Rousseau"}, {"first" : "Gopal", "last" : "Bhatt"}, {"first" : "Alvaro Pardo", "last" : "Alvarez"}, {"first" : "Dominique", "last" : "Charron"} ], "volume": "3","number": "5","pages": "190-206","abstract": "Integrated modeling of coupled surface-subsurface flow and ensuing role\r\n in diverse Earth system processes is of current research interest to\r\n characterize nonlinear rainfall-runoff response and also to understand\r\n land surface energy balances, biogeochemical processes, geomorphological\r\n dynamics, etc. A growing number of complex models have been developed\r\n for water-related research, and many of these are made available to the\r\n Earth science community. However, relatively few resources have been\r\n made accessible to the potentially large group of Earth science and\r\n engineering users. New users have to invest an extraordinary effort to\r\n study the models. To provide a stimulating experience focusing on the\r\n learning curve of integrated modeling of coupled surface-subsurface\r\n flow, we describe use cases of an open source model, the Penn State\r\n Integrated Hydrologic Model, PIHM. New users were guided through data\r\n processing and model application by reproducing a numerical benchmark\r\n problem and a real-world watershed simulation. Specifically, we document\r\n the PIHM application and its computational workflow to enable intuitive\r\n understanding of coupled surface-subsurface flow processes. In addition,\r\n we describe the user experience as important evidence of the\r\n significance of reusability. The interaction shows that documentation of\r\n data, software, and computational workflow in research papers is a\r\n promising method to foster open scientific collaboration and reuse. This\r\n study demonstrates how open science practice in research papers would\r\n promote the utility of open source software. Addressing such open\r\n science practice in publications would promote the utility of journal\r\n papers. Further, popularization of such practice will require\r\n coordination among research communities, funding agencies, and journals.", "author-email" : "xuan@udel.edu", "language" : "English", "researcherid-numbers" : "Yu, Xuan/O-3449-2014", "oa" : "DOAJ Gold, Green Accepted", "affiliation" : "Yu, X (Corresponding Author), Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n Yu, Xuan, Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n Duffy, Christopher J.; Bhatt, Gopal, Penn State Univ, Dept Civil & Environm Engn, University Pk, PA 16802 USA.\r\n Rousseau, Alain N.; Alvarez, Alvaro Pardo; Charron, Dominique, Univ Quebec, Inst Natl Rech Sci, Ctr Eau Terre Environm, INRS ETE, Quebec City, PQ, Canada.", "usage-count-last-180-days" : "0", "web-of-science-categories" : "Astronomy & Astrophysics; Geosciences, Multidisciplinary", "number-of-cited-references" : "92", "research-areas" : "Astronomy & Astrophysics; Geology", "funding-text" : "All data for this paper are properly cited and referred to in the\r\n reference list. More details of the data are available upon request from\r\n the corresponding author (xuan@udel.edu). This work was supported by NSF\r\n grants IIA-1301765, IIS-1344272, ICER-1343800, and ICER-1440323 and\r\n Shale Hills-Susquehanna Critical Zone Observatory (EAR-0725019,\r\n EAR-1239285, and EAR-1331726). The authors thank the EarthCube OntoSoft\r\n leadership for initiating the Geoscience Papers of the Future program\r\n and the early career advisory committee members. The manuscript\r\n benefited from conversations facilitated by the EarthCube Distinguished\r\n Lecturer Program. The authors also thank Yolanda Gil of University of\r\n Southern California for the insightful discussions and comments on the\r\n manuscript. We also want to thank Ibrahim Demir from University of Iowa\r\n and Runjian Wu from University of Arizona for their help with\r\n proofreading. We are very grateful for the constructive comments from\r\n reviewer Christopher Hutton and an anonymous reviewer on the earlier\r\n versions of the manuscript.", "funding-acknowledgement" : "NSFNational Science Foundation (NSF) [IIA-1301765, IIS-1344272,\r\n ICER-1343800, ICER-1440323]; Shale Hills-Susquehanna Critical Zone\r\n Observatory [EAR-0725019, EAR-1239285, EAR-1331726]; Directorate For\r\n GeosciencesNational Science Foundation (NSF)NSF - Directorate for\r\n Geosciences (GEO) [1331726] Funding Source: National Science\r\n Foundation; Division Of Earth SciencesNational Science Foundation\r\n (NSF)NSF - Directorate for Geosciences (GEO) [1331726] Funding Source:\r\n National Science Foundation; Office of Integrative ActivitiesNational\r\n Science Foundation (NSF)NSF - Office of the Director (OD) [1301765]\r\n Funding Source: National Science Foundation; Office Of The\r\n DirectorNational Science Foundation (NSF)NSF - Office of the Director\r\n (OD) [1301765] Funding Source: National Science Foundation", "times-cited" : "11", "issn" : "2333-5084", "orcid-numbers" : "Yu, Xuan/0000-0002-9055-7923\r\n Duffy, Christopher/0000-0003-0080-6445\r\n Pardo Alvarez, Alvaro/0000-0003-0302-9856\r\n Rousseau, Alain N./0000-0002-3439-2124\r\n Charron, Dominique/0000-0002-8494-1152", "usage-count-since-2013" : "11", "doc-delivery-number" : "DU9XO", "da" : "2021-03-01", "journal-iso" : "Earth Space Sci.", "keywords-plus" : "DISTRIBUTED COMPUTING ENVIRONMENT; HYDROLOGIC MODEL; CLIMATE-CHANGE;\r\n OPPORTUNITIES; SYSTEM; WORKFLOWS; GEOMORPHOLOGY; RESEARCHERS;\r\n CHALLENGES; FEEDBACKS", "unique-id" : "ISI:000382571700001", "doi" : "10.1002/2015EA000155", "bibtexKey": "yu2016science" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2dbc9c028e40c529b7fc1b4f2a8c86084/hermann", "tags" : [ "forschungsdaten","documentation","software","recommendation","diss" ], "intraHash" : "dbc9c028e40c529b7fc1b4f2a8c86084", "interHash" : "2e300fe2b524a0c4d03d7613a4dc78ce", "label" : "Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance", "user" : "hermann", "description" : "", "date" : "2021-03-01 06:20:42", "changeDate" : "2021-05-27 14:51:08", "count" : 1, "pub-type": "article", "journal": "Earth and Space Science","publisher":"American Geophysical Union (AGU)", "year": "2016", "url": "https://doi.org/10.1002%2F2015ea000136", "author": [ "Yolanda Gil","Cédric H. David","Ibrahim Demir","Bakinam T. Essawy","Robinson W. Fulweiler","Jonathan L. Goodall","Leif Karlstrom","Huikyo Lee","Heath J. Mills","Ji-Hyun Oh","Suzanne A. Pierce","Allen Pope","Mimi W. Tzeng","Sandra R. Villamizar","Xuan Yu" ], "authors": [ {"first" : "Yolanda", "last" : "Gil"}, {"first" : "Cédric H.", "last" : "David"}, {"first" : "Ibrahim", "last" : "Demir"}, {"first" : "Bakinam T.", "last" : "Essawy"}, {"first" : "Robinson W.", "last" : "Fulweiler"}, {"first" : "Jonathan L.", "last" : "Goodall"}, {"first" : "Leif", "last" : "Karlstrom"}, {"first" : "Huikyo", "last" : "Lee"}, {"first" : "Heath J.", "last" : "Mills"}, {"first" : "Ji-Hyun", "last" : "Oh"}, {"first" : "Suzanne A.", "last" : "Pierce"}, {"first" : "Allen", "last" : "Pope"}, {"first" : "Mimi W.", "last" : "Tzeng"}, {"first" : "Sandra R.", "last" : "Villamizar"}, {"first" : "Xuan", "last" : "Yu"} ], "volume": "3","number": "10","pages": "388--415", "doi" : "10.1002/2015ea000136", "bibtexKey": "gil2016toward" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24ca27c08adf7ea5e041ecda8b6be91ad/hermann", "tags" : [ "documentation","software","reusability","diss" ], "intraHash" : "4ca27c08adf7ea5e041ecda8b6be91ad", "interHash" : "3bdee2fd90af2b0755b4c42829a6d1b6", "label" : "Measuring the reusability of software components using static analysis metrics and reuse rate information", "user" : "hermann", "description" : "", "date" : "2021-02-26 07:33:26", "changeDate" : "2021-02-26 06:33:26", "count" : 2, "pub-type": "article", "journal": "Journal of Systems and Software","publisher":"Elsevier BV", "year": "2019", "url": "https://doi.org/10.1016%2Fj.jss.2019.110423", "author": [ "Michail D. Papamichail","Themistoklis Diamantopoulos","Andreas L. Symeonidis" ], "authors": [ {"first" : "Michail D.", "last" : "Papamichail"}, {"first" : "Themistoklis", "last" : "Diamantopoulos"}, {"first" : "Andreas L.", "last" : "Symeonidis"} ], "volume": "158","pages": "110423", "doi" : "10.1016/j.jss.2019.110423", "bibtexKey": "papamichail2019measuring" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f55779758f60b22189e2a3453ad74ed2/hermann", "tags" : [ "journal","documentation","data","diss" ], "intraHash" : "f55779758f60b22189e2a3453ad74ed2", "interHash" : "691c402142b189059ccf38373fef527e", "label" : "An analysis of data paper templates and guidelines: types of contextual information described by data journals", "user" : "hermann", "description" : "", "date" : "2021-02-23 06:44:07", "changeDate" : "2021-02-23 05:44:07", "count" : 1, "pub-type": "article", "journal": "Science Editing","publisher":"Korean Council of Science Editors", "year": "2020", "url": "https://doi.org/10.6087%2Fkcse.185", "author": [ "Jihyun Kim" ], "authors": [ {"first" : "Jihyun", "last" : "Kim"} ], "volume": "7","number": "1","pages": "16--23", "doi" : "10.6087/kcse.185", "bibtexKey": "kim2020analysis" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f00c070a260ea2e9a2eca96dda6f0924/hermann", "tags" : [ "forschungsdaten","documentation","software","recommendation","diss" ], "intraHash" : "f00c070a260ea2e9a2eca96dda6f0924", "interHash" : "f3617952fb4dc7d1497ed5f8b31c4e69", "label" : "Ten Simple Rules for Reproducible Computational Research", "user" : "hermann", "description" : "", "date" : "2020-03-05 11:30:25", "changeDate" : "2020-05-05 15:20:39", "count" : 3, "pub-type": "article", "journal": "PLOS Computational Biology","publisher":"Public Library of Science", "year": "2013", "url": "https://doi.org/10.1371/journal.pcbi.1003285", "author": [ "Geir Kjetil Sandve","Anton Nekrutenko","James Taylor","Eivind Hovig" ], "authors": [ {"first" : "Geir Kjetil", "last" : "Sandve"}, {"first" : "Anton", "last" : "Nekrutenko"}, {"first" : "James", "last" : "Taylor"}, {"first" : "Eivind", "last" : "Hovig"} ], "volume": "9","number": "10","pages": "1-4", "doi" : "10.1371/journal.pcbi.1003285", "bibtexKey": "sandve2013simple" } ] }